There are a number of ways global scan settings get applied to agents.
A particular scan setting can apply to all agents that the server manages or only to agents with certain scan privileges. For example, if you configure the postpone Scheduled Scan duration, only agents with the privilege to postpone Scheduled Scan will use the setting.
A particular scan setting can apply to all or only to a particular scan type. For example, on endpoints with both the Apex One server and Security Agent installed, you can exclude the Apex One server database from scanning. However, this setting applies only during Real-time Scan.
A particular scan setting can apply when scanning for either virus/malware or spyware/grayware, or both. For example, assessment mode only applies during spyware/grayware scanning.